Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate PfGW456L13_1210 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1210 Length = 374 Score = 232 bits (592), Expect = 1e-65 Identities = 118/234 (50%), Positives = 157/234 (67%), Gaps = 1/234 (0%) Query: 4 VTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIR 63 V+F + Y G + V L++ I GEFL L+GPSG GK+TSL MLAG E G I Sbjct: 15 VSFRGVQKSYDGENL-IVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 73 Query: 64 IGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKIL 123 + R + ++PP RDI MVFQNYAL+PHMTVA+N+ F L + G+ K+++ +V+ ++ Sbjct: 74 LAGRAINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGMNKSDVSARVKRVLSMV 133 Query: 124 DLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQR 183 L + R P LSGGQ+QRVA+ RA+V EPQ+ LMDEPL LD +LR + +I L + Sbjct: 134 QLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQ 193 Query: 184 RLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIG 237 RLG+T VYVTHDQ EA+TM DRVAV G +QQ+ PR +Y++P N FVA FIG Sbjct: 194 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRTLYEEPKNTFVANFIG 247 Lambda K H 0.317 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 355 Number of extensions: 12 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 374 Length adjustment: 30 Effective length of query: 347 Effective length of database: 344 Effective search space: 119368 Effective search space used: 119368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory